topology problem!

From: ramya wwjd (ramyawwjd_at_gmail.com)
Date: Fri Mar 09 2007 - 03:04:58 CST

• Next message: jieru.zheng_at_duke.edu: "question about the influence of water box size in FEP"
• Previous message: Cesar Luis Avila: "Re: Premature stop"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

hello sir,

I am working on hydrogenase(1FEH.pdb) and have to perform MD-Simulations by
NAMD. But the main problem I am facing with FES Clusters is that , these are
not present in the charmm topology file that i am using
(top_all27_prot_lipid.inp). when i generate psf and pdb by using psfgen, the
clusters were removed from the output pdb. Should I use some different
topology file for these clusters? and if so, how can i make this? can you
suggest? I will be greatful to you.
Thank you,
Ramya

• Next message: jieru.zheng_at_duke.edu: "question about the influence of water box size in FEP"
• Previous message: Cesar Luis Avila: "Re: Premature stop"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:27 CST